In my book, uninstalling isn't just "making unavailable". For the latter, renaming the *.pm files to *.pm.disabled would suffice. Uninstall means weed out the package completely *if* no other package depends on it; *or* uninstall the package along with any relying modules, recursively.

For Linux IMHO, all perl modules should be made into packages for the package manager of the distribution at hand, i.e. RPM or DEB packages. For Gentoo things might be different, haven't touched that one yet.